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Table 1 Zebrafish based conserved noncoding elements (CNE) localized onto the rainbow trout genetic maps

From: Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout

CNE Acc Dr Hs Ol Om c Ss Sa Anc Vnc
CNE152b CR846256 1 4 1 14/20    F  
CNE589–946 CR846693–CR847050 1–3 7 1–8 2 4 20 E  
CNE548–549 CR846652–CR846653 19a 8 16 16–27 1/12 35 B  
CNE594–596 CR846698–CR846700 1–3 7 8 9 11 20 E  
CNE590–591 CR846694–CR846695 3 7 1–8 2/9    E  
CNE1040–1046 CR847144–CR847150 4 7 23 11–15 24   K/GH NSe
CNE1215–1216 CR847319–CR847320 4 12 23 7–24 24 3/24 K/A NS
CNE821–822 CR846925–CR846926 5 7 23 7/15   3 K  
CNE140–141 CR846244–CR846245 6a 2 21 5/(27/31)   20 C  
CNE377–381 CR846481–CR846485 6 1 4 9/(2/29)    M/E A'E'
CNE1000–1011 CR847104–CR847115 6 1 4 24    M  
CNE270–275 CR846374–CR846379 7 11 3 10/18    J  
CNE268–274 CR846372–CR846378 7 11 3 10/18    J  
CNE432b CR846536 7–25 11 3 6    J  
CNE236–242 CR846340–CR846346 8 9 9 19    I  
CNE249–257 CR846353–CR846361 8 9 9 19    I  
CNE782–785 CR846886–CR846889 9 13 21 31 20   C  
CNE786–805 CR846890–CR846909 9 13 21 31 20 20 C  
CNE173–175 CR846277–CR846279 Unaad 15 6 27    JK  
CNE1158–1160 CR847262–CR847264 16a 3 16 27    B  
CNE210–217 CR846314–CR846321 12 10 19 17    DE  
CNE1117–1131 CR847221–CR847235 12 10 15 16–22–30 17 18 D/B B'
CNE848–849 CR846952–CR846953 13 10 15 (6/30)    D  
CNE79–83 CR846183–CR846187 13 10 15 6 16 25 D  
CNE391b CR846495 14 4 Una 3/25–18–20    G/J B'
CNE996–1102 CR847100–CR847206 5–24a 5 9–12 1–19   5 I  
CNE998–1310 CR847102–CR847414 5–24a 5 12 1/8–31 17 5 I/B A'
CNE535–540 CR846639–CR846644 16 8 16 27    B  
CNE903–904 CR847007–CR847008 16 7 16 (27/31) 1/12 6–19–23–35 B/M A'B'E'
CNE385–386 CR846489–CR846490 17 1 22 14/25    A  
CNE1056–1058 CR847160–CR847162 17 20 22 23/24 8   A/M B'
CNE170–184 CR846274–CR846288 18 15 Una Una    J  
CNE116–118 CR846220–CR846222 3–19 7–17 11–19 3/16    B  
CNE1198–1199 CR847302–CR847303 20 18 17 13/23    M  
CNE837–868 CR846941–CR846972 21 4 15 3–8–20 17   GH/I C'
CNE864–865 CR846968–CR846969 21 4 Una 8    I  
CNE1232–1235 CR847336–CR847339 21a 4 Una 8/9    I  
CNE395–396 CR846499–CR846500 5a 4 Una 19    I  
CNE765–767 CR846869–CR846871 23 1 7 21    L  
CNE523–524 CR846627–CR846628 23 12 7 12–29    L  
CNE718–719 CR846822–CR846823 24 8 20 7/19    M  
  1. Fugu CNE GenBank accession numbers (Acc), homologous chromosomal regions in zebrafish (Dr), medaka (Ol), human (Hs), rainbow trout (Om), Atlantic salmon (Ss), Arctic charr (Sa) as well as their relationship to the presumptive ancestral Actinopterygian linkage groups (Anc) are shown. Instances where the duplicate CNE map to various Anc chromosomes, the putative paralogy, based on the derived chromosomes from vertebrate ancestor (Vnc) [15], is also presented.
  2. a CNE with altered positions in zebrafish assemblies Zv6 to Zv7.
  3. b In instances where CNE were widely spaced, 15 Kbp flanking regions of human, zebrafish and fugu genomes were screened in search of homologous conserved motifs.
  4. c Rainbow trout linkage groups previously known to possess duplicated markers are separated with a forward slash '/' while linkage groups possessing duplicated CNE markers with no known previous collective affinities are indicated with a dash '-'. Duplicated pairs indicated in parentheses '()' indicate that a single CNE was localized within duplicated pseudolinkage group within a male mapping panel.
  5. d An unassigned scaffold.
  6. e Not supported based on the Nakatani et al. [15] vertebrate chromosome evolution model.